HEADER PROTEIN TRANSPORT 01-NOV-04 1XWI TITLE CRYSTAL STRUCTURE OF VPS4B COMPND MOL_ID: 1; COMPND 2 MOLECULE: SKD1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 123-444; COMPND 5 SYNONYM: VACUOLAR SORTING PROTEIN 4B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VPS4B, SKD1, VPS42; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET16B KEYWDS VPS4B, SKD1, AAA ATPASE, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.SCOTT,W.I.SUNDQUIST,C.P.HILL REVDAT 4 14-FEB-24 1XWI 1 REMARK REVDAT 3 24-FEB-09 1XWI 1 VERSN REVDAT 2 07-MAR-06 1XWI 1 JRNL REVDAT 1 11-OCT-05 1XWI 0 JRNL AUTH A.SCOTT,H.Y.CHUNG,M.GONCIARZ-SWIATEK,G.C.HILL,F.G.WHITBY, JRNL AUTH 2 J.GASPAR,J.M.HOLTON,R.VISWANATHAN,S.GHAFFARIAN,C.P.HILL, JRNL AUTH 3 W.I.SUNDQUIST JRNL TITL STRUCTURAL AND MECHANISTIC STUDIES OF VPS4 PROTEINS JRNL REF EMBO J. V. 24 3658 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 16193069 JRNL DOI 10.1038/SJ.EMBOJ.7600818 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 10917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.4110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2508 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.00000 REMARK 3 B22 (A**2) : 1.00000 REMARK 3 B33 (A**2) : -1.50000 REMARK 3 B12 (A**2) : 0.50000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.717 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.352 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.237 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.144 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2406 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3255 ; 1.723 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 6.410 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;33.002 ;23.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;20.641 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.405 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 367 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1784 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1061 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1648 ; 0.325 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 70 ; 0.195 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 41 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.173 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1529 ; 0.987 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2430 ; 1.686 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 962 ; 2.294 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 825 ; 3.804 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1XWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : SYNCHROTRON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12140 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 76.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28500 REMARK 200 R SYM FOR SHELL (I) : 0.28500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, HEPES, NACL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.04933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.52467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.28700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.76233 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 93.81167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: CRYSTAL STRUCTURE IS MONOMERIC. BIOLOGICAL FUNCTION REMARK 300 PROBABLY REQUIRES NUCLEOTIDE-DEPENDENT OLIGOMERIZATION. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 SER A 200 REMARK 475 SER A 201 REMARK 475 SER A 202 REMARK 475 ASP A 203 REMARK 475 LEU A 204 REMARK 475 VAL A 205 REMARK 475 SER A 206 REMARK 475 LYS A 207 REMARK 475 TRP A 208 REMARK 475 LEU A 209 REMARK 475 GLY A 210 REMARK 475 GLU A 211 REMARK 475 LEU A 239 REMARK 475 CYS A 240 REMARK 475 GLY A 241 REMARK 475 SER A 242 REMARK 475 ARG A 243 REMARK 475 SER A 244 REMARK 475 GLU A 245 REMARK 475 ASN A 246 REMARK 475 GLU A 247 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER A 238 N LEU A 239 1.08 REMARK 500 C GLU A 247 CA SER A 248 1.08 REMARK 500 CA GLU A 247 N SER A 248 1.17 REMARK 500 O GLU A 247 N SER A 248 1.36 REMARK 500 O SER A 238 CA LEU A 239 1.58 REMARK 500 O GLU A 211 N SER A 212 1.59 REMARK 500 O GLU A 247 CA SER A 248 1.69 REMARK 500 O GLU A 247 CB ALA A 251 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 199 C SER A 200 N -0.196 REMARK 500 VAL A 205 N VAL A 205 CA 0.121 REMARK 500 GLU A 211 C SER A 212 N -0.203 REMARK 500 GLU A 247 C SER A 248 N -0.915 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 199 CA - C - N ANGL. DEV. = 22.2 DEGREES REMARK 500 ILE A 199 O - C - N ANGL. DEV. = -22.7 DEGREES REMARK 500 LEU A 204 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU A 209 CA - C - N ANGL. DEV. = -12.9 DEGREES REMARK 500 GLU A 211 CA - C - N ANGL. DEV. = 18.2 DEGREES REMARK 500 GLU A 211 O - C - N ANGL. DEV. = -38.1 DEGREES REMARK 500 ASP A 237 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 SER A 238 O - C - N ANGL. DEV. = -70.7 DEGREES REMARK 500 GLU A 245 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 GLU A 247 CA - C - N ANGL. DEV. = -80.4 DEGREES REMARK 500 GLU A 247 O - C - N ANGL. DEV. = -22.7 DEGREES REMARK 500 SER A 248 C - N - CA ANGL. DEV. = 100.6 DEGREES REMARK 500 ASP A 340 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 347 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 166 178.62 -55.98 REMARK 500 SER A 202 127.60 100.43 REMARK 500 ASP A 203 -102.67 -113.92 REMARK 500 TRP A 208 -143.71 -171.54 REMARK 500 SER A 212 -28.50 150.75 REMARK 500 CYS A 240 -1.72 -43.33 REMARK 500 GLU A 245 -148.04 -129.66 REMARK 500 ASN A 246 -85.96 -119.85 REMARK 500 GLU A 247 110.30 96.12 REMARK 500 GLU A 249 -91.21 -82.05 REMARK 500 VAL A 265 -89.77 -71.14 REMARK 500 LEU A 300 155.05 -45.44 REMARK 500 LEU A 312 -86.68 -48.02 REMARK 500 HIS A 313 -32.27 -33.96 REMARK 500 ASP A 334 114.38 -37.34 REMARK 500 ASP A 379 47.80 -156.32 REMARK 500 PRO A 389 102.36 -55.03 REMARK 500 ALA A 391 88.86 -64.86 REMARK 500 GLU A 438 -80.31 -69.39 REMARK 500 ASP A 439 28.93 -67.27 REMARK 500 PHE A 440 -41.34 -148.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 211 SER A 212 -115.65 REMARK 500 GLU A 247 SER A 248 -111.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 211 -32.73 REMARK 500 SER A 238 -57.92 REMARK 500 GLU A 247 -92.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 DBREF 1XWI A 123 444 UNP O75351 VPS4B_HUMAN 123 444 SEQRES 1 A 322 ALA ILE VAL ILE GLU ARG PRO ASN VAL LYS TRP SER ASP SEQRES 2 A 322 VAL ALA GLY LEU GLU GLY ALA LYS GLU ALA LEU LYS GLU SEQRES 3 A 322 ALA VAL ILE LEU PRO ILE LYS PHE PRO HIS LEU PHE THR SEQRES 4 A 322 GLY LYS ARG THR PRO TRP ARG GLY ILE LEU LEU PHE GLY SEQRES 5 A 322 PRO PRO GLY THR GLY LYS SER TYR LEU ALA LYS ALA VAL SEQRES 6 A 322 ALA THR GLU ALA ASN ASN SER THR PHE PHE SER ILE SER SEQRES 7 A 322 SER SER ASP LEU VAL SER LYS TRP LEU GLY GLU SER GLU SEQRES 8 A 322 LYS LEU VAL LYS ASN LEU PHE GLN LEU ALA ARG GLU ASN SEQRES 9 A 322 LYS PRO SER ILE ILE PHE ILE ASP GLU ILE ASP SER LEU SEQRES 10 A 322 CYS GLY SER ARG SER GLU ASN GLU SER GLU ALA ALA ARG SEQRES 11 A 322 ARG ILE LYS THR GLU PHE LEU VAL GLN MET GLN GLY VAL SEQRES 12 A 322 GLY VAL ASP ASN ASP GLY ILE LEU VAL LEU GLY ALA THR SEQRES 13 A 322 ASN ILE PRO TRP VAL LEU ASP SER ALA ILE ARG ARG ARG SEQRES 14 A 322 PHE GLU LYS ARG ILE TYR ILE PRO LEU PRO GLU PRO HIS SEQRES 15 A 322 ALA ARG ALA ALA MET PHE LYS LEU HIS LEU GLY THR THR SEQRES 16 A 322 GLN ASN SER LEU THR GLU ALA ASP PHE ARG GLU LEU GLY SEQRES 17 A 322 ARG LYS THR ASP GLY TYR SER GLY ALA ASP ILE SER ILE SEQRES 18 A 322 ILE VAL ARG ASP ALA LEU MET GLN PRO VAL ARG LYS VAL SEQRES 19 A 322 GLN SER ALA THR HIS PHE LYS LYS VAL ARG GLY PRO SER SEQRES 20 A 322 ARG ALA ASP PRO ASN HIS LEU VAL ASP ASP LEU LEU THR SEQRES 21 A 322 PRO CYS SER PRO GLY ASP PRO GLY ALA ILE GLU MET THR SEQRES 22 A 322 TRP MET ASP VAL PRO GLY ASP LYS LEU LEU GLU PRO VAL SEQRES 23 A 322 VAL SER MET SER ASP MET LEU ARG SER LEU SER ASN THR SEQRES 24 A 322 LYS PRO THR VAL ASN GLU HIS ASP LEU LEU LYS LEU LYS SEQRES 25 A 322 LYS PHE THR GLU ASP PHE GLY GLN GLU GLY HET SO4 A 601 5 HET SO4 A 602 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *9(H2 O) HELIX 1 1 LYS A 132 VAL A 136 5 5 HELIX 2 2 LEU A 139 PHE A 156 1 18 HELIX 3 3 PRO A 157 PHE A 160 5 4 HELIX 4 4 GLY A 179 ALA A 191 1 13 HELIX 5 5 SER A 212 ASN A 226 1 15 HELIX 6 6 ASP A 237 GLY A 241 5 5 HELIX 7 7 GLU A 249 GLY A 264 1 16 HELIX 8 8 ASP A 285 ARG A 291 1 7 HELIX 9 9 GLU A 302 GLY A 315 1 14 HELIX 10 10 THR A 322 LYS A 332 1 11 HELIX 11 11 SER A 337 MET A 350 1 14 HELIX 12 12 MET A 350 ALA A 359 1 10 HELIX 13 13 THR A 395 VAL A 399 5 5 HELIX 14 14 PRO A 400 LEU A 404 5 5 HELIX 15 15 SER A 410 ASN A 420 1 11 HELIX 16 16 ASN A 426 ASP A 439 1 14 SHEET 1 A 6 VAL A 125 GLU A 127 0 SHEET 2 A 6 THR A 195 SER A 200 -1 O SER A 198 N VAL A 125 SHEET 3 A 6 SER A 229 ASP A 234 1 O PHE A 232 N PHE A 197 SHEET 4 A 6 ILE A 272 THR A 278 1 O LEU A 275 N ILE A 231 SHEET 5 A 6 GLY A 169 PHE A 173 1 N LEU A 172 O GLY A 276 SHEET 6 A 6 LYS A 294 TYR A 297 1 O LYS A 294 N LEU A 171 SHEET 1 B 3 LEU A 376 PRO A 383 0 SHEET 2 B 3 HIS A 361 PRO A 368 -1 N GLY A 367 O VAL A 377 SHEET 3 B 3 ALA A 391 GLU A 393 -1 O ILE A 392 N PHE A 362 CISPEP 1 LYS A 227 PRO A 228 0 -2.75 SITE 1 AC1 5 PRO A 176 GLY A 177 THR A 178 GLY A 179 SITE 2 AC1 5 LYS A 180 SITE 1 AC2 6 HIS A 304 ARG A 327 ARG A 331 PRO A 400 SITE 2 AC2 6 GLY A 401 ASP A 402 CRYST1 88.058 88.058 112.574 90.00 90.00 120.00 P 65 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011356 0.006556 0.000000 0.00000 SCALE2 0.000000 0.013113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008883 0.00000